ABSTRACT The overarching goal of our LINCS project (U54HG008097) is to test the hypothesis that modulation of phosphorylation-mediated signaling events in response to perturbations can establish new cellular states by altering their phosphoproteomic and epigenetic landscapes. To achieve this goal, we propose performing mass spectrometry (MS)- based proteomic assays that specifically target quantitative readouts of phosphosignaling and chromatin modifications in cells on > 15,000 perturbational conditions. These perturbations will focus on modulation of signaling cascades and epigenetic marks by small molecules and genetic manipulations. We will study several different cellular model systems, including comprehensive studies of neuronal lineage differentiation starting from stem cells. We have established a center with the necessary infrastructure, pipelines, data management, and analytics required to perform the largest set of related experiments with MS proteomic read outs to date. We also employ next- generation MS acquisition technologies to establish a permanently minable MS data resource that will be accessible to the public. We contribute the resulting data and tools to the Library of Integrated Network-based Cellular Signatures (LINCS) program for the purpose of making connections among disparate perturbations through phosphoproteomic and chromatin modification signatures in concert with other data types to be contributed to LINCS by other centers. The resulting analyses help identify novel therapeutic opportunities and synergies, as dysregulation of phosphosignaling and epigenetic systems are two of the most common molecular etiologies identified in a growing number of genetic, developmental, and environmental diseases. In this supplement request we will study a unique model of Alzheimer's etiology derived from cell lines obtained from Down syndrome patients. We will test how cells with triplication of chromosome 21 respond differentially to kinase inhibitor stimuli from their otherwise isogenic disomic counterparts. We will measure aspects of signaling and epigenetics using proteomic analyses (P100 and GCP), and transcriptional responses using RNA-Seq and L1000 assays for maximum compatibility with the body of existing LINCS data.